Let's first turn on the cache for increased performance and improved styling
# Set some global knitr options
library("knitr")
opts_chunk$set(tidy=TRUE, tidy.opts=list(blank=FALSE, width.cutoff=60), cache=TRUE, messages=FALSE)
Friday, November 6
Let's first turn on the cache for increased performance and improved styling
# Set some global knitr options
library("knitr")
opts_chunk$set(tidy=TRUE, tidy.opts=list(blank=FALSE, width.cutoff=60), cache=TRUE, messages=FALSE)
Hybridization

about 20 probes that “perfectly” represent the gene (Perfect Match)
about 20 probes that do not match the gene sequence (Mismatch)
Probeset
For a valid gene expression measurement the Perfect Match sticks and the Mistach does not!
Let's watch a small video
(Source: http://www.mouseclinic.de/)
| cDNA microarray | Affymetrix | Illumina |
|---|---|---|
| 1 probe/gene | 1-20 probes/gene | 30 beads(probes)/gene |
| Probe of variable lengths | 25-mer probes | 50-mer probes |
| Two colors | One color | One color |
| Flexible, choice of probes | High density/Replication | High density/Replication |
| - | Cross hybridization | - |
Most of these steps require the use of statistical methods and/or computational tools
Note: Even though microarrays were designed to study gene expression, they can be used to study many other things (DNA-protein binding, methylation, splicing, etc). Though they are slowly being replaced by sequencing-based assays.